If your pond is pea soup green, do not clean it with an algae bloom unless there more than 1" of debris in the bottom of the pond.
New pond water and green water typically cycles through an algae bloom with the addition of plants as the temperature rises and the growth of beneficial bacteria in the filter. However, removing the debris that has settled to the bottom of the pond will reduce the organic load on the water environment and allow your pond to clear. Fish also stir up the debris on the pond floor. This creates a constant appearance of cloudy water due to the suspended particles in the water.

To clean your pond, you will need a large trash can or wading pool, as a holding tank while cleaning the pond. Be sure to cover the holding tank because fish often jump out of a new home. The general rule is one gallon of water for every one inch of fish. Fish over four inches should have the water aerated with a pump or aeration system. Fill the container with water from the pond before you do anything to stir up the sediment from the bottom. Set your container in the shade and add a few submerged plants for some oxygen.

Empty the pond halfway, either by siphoning the water through a hose or by pumping it out with a submersible pump. While you are draining the water, lift out your plants. The oxygenating or submerged plants can be placed in a bucket of water. Put all your plants in the shade and cover them with wet newspaper to keep the leaves moist. Once you have your plants out and the pond emptied to about six inches, you can start to catch your fish. This is very stressful for the fish, so proceed quietly and try to gently trap them in one corner of the pond. Avoid chasing them throughout the length of the pond if possible. If the water level is too low the fish may be injured in their own gaseous waste. You may put your snails in the same container as the fish. Bail out the remaining water. You can use a dustpan and brush or a wet/dry vacuum. Refill the pond as soon as possible. Treat the water with a dechlorinator that will correct CHLOROMINES as well as chlorine, which is frequently added to local water. Add back several buckets of the original pond water. This will inoculate the freshly cleaned pond with necessary microorganisms. Also jump start your filtration with the addition of a packaged beneficial bacteria. Place the hardy lilies and submerged plants back in the pond. The hardy bog plants can be set back in their original places. This is the perfect time to repot and fertilize your aquatic plants.

There are two ways to reintroduce your fish to the pond. One way is to pump the clean water into the holding tank until its water is with in five degrees of the water in the pond. The other way is to place the fish in a large plastic fish bag of water from the holding tank and float the bag in the shade on the pond surface. If there is no shade cover the bag with a cloth. The fish should be floated no longer than fifteen minutes. Then slowly mix new pond water into the bag to acclimate the fish to their new environment.